welcome to introduction to bioinformatics intro to scenario 8 identification of genes of foreign...

Welcome toIntroduction to BioinformaticS

• Intro to Scenario 8 Identification of genes of foreign origin

Scenario 1Comparison of genomes of

pathogenic and nonpathogenic E. coli

E. coli K12 E. coli O157:H7

E. coli: What makes it kill?

Gene finder

TCTACTTATA TTCAATCCAC AGGGCTACACAAGAGTCTGT TGAATGAACA CATACATGGTTTCTGTCTGC TCTGACCTCT GGCAGCTTTC TGGATTTCGG AACTCTAGCC TGCCCCACTC GAACCTTAGT GACTTCTGCT ATACCAAAGT CTCCGTAAAC CTCTAACATG ATGTCAGCAA TGAATAAACT TTGTTAAAGG TACAAATGAA AAGAGTTTAA AGTTAAAAAC GAATTGCAGT AAACCTGTAT GGTTACATGA ACTGCCTAAA TTATATATTT TAAGAAATTA ATTGCAATTA CCCCAGCTGT CATTAAAAAG AGGCAAATAC GACAGCACTG ACCCTCAAGA AGGCACCGGC GCTGAAATTC CGCTGAGAGC AGAGTGGTAC CCCTGCACCA GGTCTTTCCT GTGGGCACTG ATGAATGACT GAACGAACGA TTGAATGAAA

Gene finder


Blast + parser

Pathogenspecific

(~1000!) ?

Pathogenosisspecific


DNA Pathogen

Nonpathogen

Virus-related genes

Disease-related genes

Pathogenecity Islands (PAI)


Gene finder


Gene finder


Blast + parser

Pathogenspecific

(~1000!) ?

Pathogenosisspecific

foreign genes

How to find foreign genes?

Current methods• % GC

• Dinucleotide frequencies

• Codon bias

• Amino acid bias



0.29274613 0.27824858 0.32350427 0.321013 0.282145770.24678363 0.3089947 0.32791328 0.2984127 0.328798170.2797619 0.3152174 0.46096095 0.31343284 0.343434330.32916668 0.37955555 0.26495728 0.28431374 0.321937320.29405162 0.26300985 0.3646139 0.29989868 0.335164840.36720142 0.3510848 0.31604227 0.2984234 0.230240550.34567901 0.34285715 0.38206628 0.33838382 0.323809530.28865057 0.33333334 0.2717087 0.33004925 0.315466230.29333332 0.3200222 0.3412162 0.32882375 0.299435020.35947713 0.32882884 0.34351662 0.26504064 0.325062040.39583334 0.29283488 0.47674417 0.296 0.307493540.3116883 0.2754821 0.30488145 0.36578172 0.289922480.6219512 0.37037036 0.29738563 0.42553192 0.361200420.26923078 0.3197176 0.27430555 0.32748538 0.321782170.28615862 0.30438185 0.272578 0.32188296 0.352737370.28374657 0.3477868 0.31501833 0.31860465 0.29528160.2905983 0.3215859 0.3195021 0.29113925 0.34328360.30982906 0.34751773 0.35598704 0.30678466 0.329004320.29574862 0.30287206 0.3068182 0.3878205 0.34693880.25382262 0.34519956 0.3283208 0.26345214 0.2958245...

%GC of genes of Prochlorococcus




• Codon bias

• Amino acid bias

How to find foreign genes?Dinucleotide frequencies

Gene from Prochlorococcus marinus MED4ATGGAGATTGTTTGTAATCAAAATGAATTTAATTATGCTATTCAATTAGTTAGTAAAGCAGTTGCTTCAAGACCTACGCATCCTATCCTTGCAAATTTACTTCTAACAGCTGATCAAGGTACTAATAAAATTAGTTTAACTGGATTTGATTTGAATCTAGGAATACAAACTTCATTTGATGCAACTGTAAACAAAAGTGGAGCAATTACAATTCCATCTAAACTTTTATCTGAAATAGTTAATAAACTACCAAGCGAAACTCCTGTCTCTCTTGATGTTGATGAGAGTTCTGACAATATTTTAATTAAAAGTGATAGGGGTTCTTTTAATATTAAAGGTATTCCATCAGACGATTACCCAAGCTTACCGTTTGTAGAAAGTGGTACATCTTTGAATATTGATCCAAGTTCTTTTTTAAAAGCTTTAAAATTAACTATATTCGCTAGTAGTAGTGATGATTCAAAGCAATTACTCACAGGAGTAAATTTTACATTTAATTTAAAATATTTGGAGTCAGCTGCAACAGATGGGCATAGATTGGCTGTTGTTTTGGTTGATAACAAAGAAAATTTTGATGAAAAAGAAGATTTTGCTTCAAATGAAGAAAACTTATCAGTTACTATACCAACAAGATCTTTAAGAGAAATTGAAAAGCTTGTTAGCCTTAGAAGTTCTGAAAATTCAATTAAACTTTTCTATGACAAAGGTCAAGTAGTATTTATTTCCTCTAATCAAATAATTACTACTAGAACCCTTGAAGGTTCTTATCCAAATTATTCTCAATTAATACCTGATAATTTTACTAAAATTTTTACATTTAATACAAAAAAAATAATCGAATCACTTGAAAGAATAGCAGTTTTAGCAGACCAACAAAGTAGTGTCGTTAAGATTAAACTTAATGAAAAGGATTTAGCATTAGTCAGTGCTGATGCTCAAGACATAGGGAATGCCAGCGAATTAGTTCCTGTATCTTTTTATTTTGATCAATTTGATATAGCTTTTAATGTAAGGTATTTATTAGAAGGTTTAAAAGTTATATCAAGTGAAAATGTAATTTTTAAATGTAATCTTCCAACTACTCCAGCTGTTTTAGTTCCAGAAGATAATATTAATTCTTTTACGTATTTAGTCATGCCTGTTCAAGTCCGTTCTTAA

A C G T

A 167 47 80 116

C 61 26 10 65

G 65 30 23 59

T 117 59 64 168

ρ*XY = f*XY / f*X f*Y


Study Question 3:Calculate ρ*AA in the following 50-nt sequence:

TGATGACAGTCGATTTTTCGGTAGGATAACTGCCATGCCTCTCAAAGTAC

ρ*XY = f*XY / f*X f*Y


δ* (f, g) = (1/16) Σ | ρ*XY(f) - ρ*XY(g) |


δ* (f, g) = (1/16) Σ | ρ*XY(f) - ρ*XY(g) |

Calculate δ*(human,mouse)?




• Codon bias

• Amino acid bias


Cholera toxin locus 100 kbases




• Codon bias

• Amino acid bias




• Codon bias

• Amino acid bias

Good for large blocks of nucleotides

Not as good for individual genes

Need an indicator more information-dense

How to find foreign genes?Markov Models

AAAA: 10%

AAAC: 15%

AAAG: 40%

AAAT: 35%

AAAAACAAGAATACA . . .TTGTTT

TrainingSet

Building the model


Building the model

AACA: 25%

AACC: 45%

AACG: 25%

AACT: 5%

AAAAACAAGAATACA . . .TTGTTT

TrainingSet


Using the model

A C G TAAA 0.10 0.15 0.40 0.35AAC 0.25 0.45 0.25 0.05AAG 0.25 0.20 0.30 0.25 AAT 0.25 0.20 0.30 0.25 ACA 0.15 0.20 0.25 0.40 . . .TTG 0.20 0.50 0.05 0.25TTT 0.10 0.55 0.25 0.10

Candidategene

AAAACAA…

0.10

3rd order Markov model

Analyze sequence model

Compare test sequence to model

Produce new sequence per model


Analyze sequence model

Produce new sequence per model


Take a test run through

Hamlet.pl

Scenario 8Gene Identification

How do you tell if an orf is real?

Genetic CodeUUU Phe UCU Ser UAU Tyr UGU CysUUC Phe UCC Ser UAC Tyr UGC CysUUA Leu UCA Ser UAA ochre UGA opalUUG Leu UCG Ser UAG amber UGG TrpCUU Leu CCU Pro CAU His CGU ArgCUC Leu CCC Pro CAC His CGC ArgCUA Leu CCA Pro CAA Gln CGA ArgCUG Leu CCG Pro CAG Gln CGG ArgAUU Ile ACU Thr AAU Asn AGU SerAUC Ile ACC Thr AAC Asn AGC SerAUA Ile ACA Thr AAA Lys AGA ArgAUG Met ACG Thr AAG Lys AGG ArgGUU Val GCU Ala GAU Asp GGU GlyGUC Val GCC Ala GAC Asp GGC GlyGUA Val GCA Ala GAA Glu GGA GlyGUG Val GCG Ala GAG Glu GGG Gly

The code is degenerate

Are codons equally used?



Genetic Code (human)UUU Phe UCU Ser UAU Tyr UGU CysUUC Phe UCC Ser UAC Tyr UGC CysUUA Leu UCA Ser UAA ochre UGA opalUUG Leu UCG Ser UAG amber UGG TrpCUU Leu CCU Pro CAU His CGU ArgCUC Leu CCC Pro CAC His CGC ArgCUA Leu CCA Pro CAA Gln CGA ArgCUG Leu CCG Pro CAG Gln CGG ArgAUU Ile ACU Thr AAU Asn AGU SerAUC Ile ACC Thr AAC Asn AGC SerAUA Ile ACA Thr AAA Lys AGA ArgAUG Met ACG Thr AAG Lys AGG ArgGUU Val GCU Ala GAU Asp GGU GlyGUC Val GCC Ala GAC Asp GGC GlyGUA Val GCA Ala GAA Glu GGA GlyGUG Val GCG Ala GAG Glu GGG Gly

The third position is biased

Most frequently used codons



ATGCGGTGGGCCCAACCACATCGTGGGCAGTCCCTT

Genetic Code (human)UUU Phe UCU Ser UAU Tyr UGU CysUUC Phe UCC Ser UAC Tyr UGC CysUUA Leu UCA Ser UAA ochre UGA opalUUG Leu UCG Ser UAG amber UGG TrpCUU Leu CCU Pro CAU His CGU ArgCUC Leu CCC Pro CAC His CGC ArgCUA Leu CCA Pro CAA Gln CGA ArgCUG Leu CCG Pro CAG Gln CGG ArgAUU Ile ACU Thr AAU Asn AGU SerAUC Ile ACC Thr AAC Asn AGC SerAUA Ile ACA Thr AAA Lys AGA ArgAUG Met ACG Thr AAG Lys AGG ArgGUU Val GCU Ala GAU Asp GGU GlyGUC Val GCC Ala GAC Asp GGC GlyGUA Val GCA Ala GAA Glu GGA GlyGUG Val GCG Ala GAG Glu GGG Gly

Most frequently used codons

PSSM for third position?

If AT G

If CG G C A T

Third order Markov Chain

welcome to introduction to bioinformatics intro to scenario 8 identification of genes of foreign...

Documents

coli o157

coli k12e

identification of genes

foreign origin scenario

current methods

bioinformatics intro

comparison of genomes